Table 1.

MaxQuant/Perseus filtering and imputation strategies used in Figure 3 and Figure 4.

Strategy	Filtering on valid values	Missing value imputation	False Discovery Rate Estimation
Strategy 1	3 valid values in total	Imputed from total matrix with width=0.5, down-shift=1.5	Permutation; num. randomizations = 250
Strategy 2	4 valid values in at least one group	Imputed from total matrix with width=0.5, down-shift=1.5	Permutation; num. randomizations = 250
Strategy 3	2 valid values from both groups (required to perform the t-test)	No imputation	Permutation; num. randomizations = 250
Strategy 4	2 valid values in both groups	Imputed from total matrix with width=0.5, down-shift=1.5	Permutation; num. randomizations = 250
Strategy 5	No filter	Imputed from total matrix with width=0.5, down-shift=1.5	Permutation; num. randomizations = 250